A production molecular dynamics run is not just “the next button” after equilibration. It is the point where a prepared system becomes a trajectory you may rely on for analysis—and small setup mismatches can make that handoff harder to interpret. A useful habit is to treat the transition from equilibration to production as a short checklist: confirm the input, carry forward compatible parameters, choose the right compute route, and decide how you want to inspect the results.
Start with the equilibrated system you actually want
Before launching production MD in GROMACS Wizard, complete NPT equilibration and verify that the equilibrated system is the one you intend to continue. Production can take either a GRO file from equilibration or a previous production run, or an equilibrated batch project. If you are continuing from the previous step, the auto-fill control can populate the input path from the prior successful project. You can also select a GRO file yourself.
This simple input check helps prevent a common workflow snag: running the right parameters on the wrong starting structure. If you use batch projects, the batch-computations tutorial explains that route.
Keep the coupling settings consistent
The Parameters section exposes frequently adjusted choices, such as the integration time step and number of steps. Other GROMACS options are available through All…, where you can review or customize advanced parameters. Position-restraint options are filled automatically based on the input system.
One particularly important check is continuity with equilibration: temperature-coupling parameters should correspond to those used for NVT equilibration, and pressure-coupling parameters should correspond to NPT equilibration. If velocity generation is enabled, check that its temperature is consistent as well. These are not settings to change casually just because a production run is starting; review them against the preceding stages of your workflow.
For the tutorial, the documented example resets parameters to their defaults and sets the maximum number of steps to 50,000 so the run finishes quickly. Treat that number as a tutorial choice, not a general recommendation for every scientific question or system.
The advanced-parameter window can reset values, load parameters from an MDP file, or save them to an MDP file. Modified parameters are saved when SAMSON closes, so if you return later, check that the values shown are the ones you intend to use.
Choose where the work should run
GROMACS Wizard offers three routes: generate inputs for use elsewhere, simulate locally on your PC, or simulate in the cloud. Local execution is convenient when your computer is suitable for the job. Cloud execution may suit larger systems that need more resources, and requires computing credits. Generating inputs is useful when you want a ready-to-use project to run on a cluster, for example.
For a local run, progress appears in the Output window. You can continue using SAMSON while calculations run, and check job status later through Local jobs. If you launch several jobs or a batch job, use that job list to follow their state rather than expecting a single completion prompt.
Plan the results import before the run ends
When results are imported, GROMACS Wizard can offer options for RMSD and radius-of-gyration plots, as well as choices for trajectory import. You can import the whole trajectory, only its last frame, or a selected frame range; you can also choose periodic-boundary-condition treatment and what to center the system on—for example, the protein.
Think about what you need to inspect before choosing. A full trajectory is useful when you need to examine motion across frames; importing a smaller selection may be more convenient when your immediate goal is a quick structural check. If you do not want to import the trajectory, choosing Cancel does not delete the results and still allows the plot to be generated.
After the job finishes and results are loaded, the radius-of-gyration and RMSD plots are generated. Pulling simulations also produce plots for pull force and coordinates. You can save a plot using the Save button above the figure. Results are stored in the configured results folder; production-run folders use the suffix _md and include the launch date and time.
The practical takeaway: verify what you are continuing from, check the coupling settings against equilibration, and decide what you need from the trajectory before starting. For the full walkthrough, see the GROMACS Wizard production MD tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.